unmapped reads in demultiplexed bam

          path = outpath + bc + "." + label + '.demx.bam'

        bcfilehandles[bc] = pysam.AlignmentFile(path, "wb", template=inbam, threads = pout)

    for read in inbam.fetch(contig=chr):

    for read in inbam.fetch(contig=chr, until_eof=True):

        thisBC = read.get_tag("BC")

        if thisBC in bcfilehandles:

            bcfilehandles[thisBC].write(read)

# Pipeline to run UMI-seq analysis from fastq to read count tables.

# Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann

# Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se

vers=2.9.4g

vers=2.9.4h

currentv=$(curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/main/zUMIs.sh | grep '^vers=' | cut -f2 -d "=")

if [ "$currentv" != "$vers" ] ; then

    echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------";